Module merge_dwis has no output called out_dwi_phase

[Gail Harmata]

Summary

I am trying to run qsiprep on data without a phase file, and I am getting this error:
Exception: Some connections were not found
Module merge_dwis has no output called out_dwi_phase

The variable "out_dwi_phase" appears in merge.py on line 295. I don't see it being optional based on the variable use_phase, so I think it is preventing me from being able to use qsiprep. However, I could be misunderstanding the code. I also posted this on NeuroStars here, but no one has responded as of 7/9/2024.

Additional details

• QSIPrep version: qsiprep v0.21.5.dev0+g36b93fe.d20240504 (pulled from docker://pennbbl/qsiprep:0.21.4)
• Apptainer version: 1.3.0-1.el7

What were you trying to do?

Run qsiprep from a container on an HPC system without a phase file.

What did you expect to happen?

The dwi file to go through all preprocessing steps.

What actually happened?

The code aborts quickly and gives the following error message:

40703-16:06:45,407 nipype.workflow INFO:
	 Running with omp_nthreads=8, nthreads=56
240703-16:06:45,447 nipype.workflow IMPORTANT:
	 
    Running qsiprep version 0.21.5.dev0+g36b93fe.d20240504:
      * BIDS dataset path: /mnt/share/Bipolar_MDD/Bipolar_MDD_Data.
      * Participant list: ['23522001'].
      * Run identifier: 20240703-155819_1a1f0185-d6ec-4956-bc3a-1c7e2f804d08.
    
240703-16:08:55,333 nipype.workflow INFO:
	 Running nonlinear normalization to template
240703-16:09:09,952 nipype.workflow INFO:
	 [{'dwi_series': ['/mnt/share/Bipolar_MDD/Bipolar_MDD_Data/sub-23522001/ses-20230127s3T/dwi/sub-23522001_ses-20230127s3T_acq-Multi_dwi.nii.gz'], 'fieldmap_info': {'suffix': None}, 'dwi_series_pedir': 'j-', 'concatenated_bids_name': 'sub-23522001_ses-20230127s3T_acq-Multi'}]
240703-16:09:10,452 nipype.workflow IMPORTANT:
	 Creating dwi processing workflow "dwi_preproc_ses_20230127s3T_acq_Multi_wf" to produce output sub-23522001_ses-20230127s3T_acq-Multi (1.58 GB / 110 DWIs). Memory resampled/largemem=3.33/3.91 GB.
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 1091, in build_qsiprep_workflow
    retval["workflow"] = init_qsiprep_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 237, in init_qsiprep_wf
    single_subject_wf = init_single_subject_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 748, in init_single_subject_wf
    dwi_preproc_wf = init_dwi_preproc_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/base.py", line 363, in init_dwi_preproc_wf
    pre_hmc_wf = init_dwi_pre_hmc_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/pre_hmc.py", line 320, in init_dwi_pre_hmc_wf
    merge_dwis = init_merge_and_denoise_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/merge.py", line 345, in init_merge_and_denoise_wf
    workflow.connect([
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 239, in connect
    raise Exception("\n".join(["Some connections were not found"] + infostr))
Exception: Some connections were not found
Module merge_dwis has no output called out_dwi_phase

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/managers.py", line 599, in _run_server
    server.serve_forever()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/managers.py", line 184, in serve_forever
    sys.exit(0)
SystemExit: 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 300, in _run_finalizers
    finalizer()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 224, in __call__
    res = self._callback(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 133, in _remove_temp_dir
    rmtree(tempdir)
  File "/opt/conda/envs/qsiprep/lib/python3.10/shutil.py", line 725, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/opt/conda/envs/qsiprep/lib/python3.10/shutil.py", line 681, in _rmtree_safe_fd
    onerror(os.unlink, fullname, sys.exc_info())
  File "/opt/conda/envs/qsiprep/lib/python3.10/shutil.py", line 679, in _rmtree_safe_fd
    os.unlink(entry.name, dir_fd=topfd)
OSError: [Errno 16] Device or resource busy: '.nfs00000000051647cb0000042c'
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 300, in _run_finalizers
    finalizer()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 224, in __call__
    res = self._callback(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/util.py", line 133, in _remove_temp_dir
    rmtree(tempdir)
  File "/opt/conda/envs/qsiprep/lib/python3.10/shutil.py", line 731, in rmtree
    onerror(os.rmdir, path, sys.exc_info())
  File "/opt/conda/envs/qsiprep/lib/python3.10/shutil.py", line 729, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tmp/pymp-w6bcbgw0'

Reproducing the bug

Bash script

#!/bin/bash

#run qsiprep with patch2self, eddy, SyN-based susceptibility distortion correction

qsiprep \
/mnt/share/Bipolar_MDD/Bipolar_MDD_Data /mnt/share/Bipolar_MDD/derivatives/qsiprep/00_preprocessed_dwi participant \
--ignore phase \
--skip_bids_validation \
--separate_all_dwis \
--participant-label 23522001 \
--anat-modality T1w \
--output-resolution 1.7 \
--denoise-method patch2self \
--unringing-method mrdegibbs \
--b1-biascorrect-stage final \
--denoise-after-combining \
--distortion-group-merge average \
--anatomical-template MNI152NLin2009cAsym \
--b0-to-t1w-transform Affine \
--intramodal-template-transform Affine \
--fs-license-file /mnt/share/Programs/FreeSurfer7.2/freesurfer/license.txt \
--b0-motion-corr-to iterative \
--hmc-transform Affine \
--hmc_model eddy \
--use-syn-sdc \
--verbose \
--work_dir /mnt/share/Bipolar_MDD/derivatives/qsiprep/temp 

HPC job script

#!/bin/bash
#$ -pe smp 16
#$ -q PINC,UI
#$ -m bea
#$ -M [e-mail]
#$ -j y
#$ -o /Shared/MRRCdata/Bipolar_MDD/scripts/qsiprep/00_preprocessing/out
singularity exec -c -W /nfsscratch/Users/gharmata/ -B /Shared/MRRCdata:/mnt/share /Shared/MRRCdata/Programs/qsiprep/qsiprep-v0.21.4.sif /mnt/share/Bipolar_MDD/scripts/qsiprep/00_preprocessing/job_scripts/sub-23522001_ses-20230127s3T_0.sh